1
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Vitale GA, Geibel C, Minda V, Wang M, Aron AT, Petras D. Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products. Nat Prod Rep 2024; 41:885-904. [PMID: 38351834 PMCID: PMC11186733 DOI: 10.1039/d3np00050h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Indexed: 06/20/2024]
Abstract
Covering: 1995 to 2023Advances in bioanalytical methods, particularly mass spectrometry, have provided valuable molecular insights into the mechanisms of life. Non-targeted metabolomics aims to detect and (relatively) quantify all observable small molecules present in a biological system. By comparing small molecule abundances between different conditions or timepoints in a biological system, researchers can generate new hypotheses and begin to understand causes of observed phenotypes. Functional metabolomics aims to investigate the functional roles of metabolites at the scale of the metabolome. However, most functional metabolomics studies rely on indirect measurements and correlation analyses, which leads to ambiguity in the precise definition of functional metabolomics. In contrast, the field of natural products has a history of identifying the structures and bioactivities of primary and specialized metabolites. Here, we propose to expand and reframe functional metabolomics by integrating concepts from the fields of natural products and chemical biology. We highlight emerging functional metabolomics approaches that shift the focus from correlation to physical interactions, and we discuss how this allows researchers to uncover causal relationships between molecules and phenotypes.
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Affiliation(s)
- Giovanni Andrea Vitale
- CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tuebingen, Tuebingen, Germany
| | - Christian Geibel
- CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tuebingen, Tuebingen, Germany
| | - Vidit Minda
- Division of Pharmacology and Pharmaceutical Sciences, University of Missouri - Kansas City, Kansas City, USA
- Department of Chemistry and Biochemistry, University of Denver, Denver, USA.
| | - Mingxun Wang
- Department of Computer Science, University of California Riverside, Riverside, USA.
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, USA.
| | - Daniel Petras
- CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tuebingen, Tuebingen, Germany
- Department of Biochemistry, University of California Riverside, Riverside, USA.
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2
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Palermo G, Schouten WM, Alonso LL, Ulens C, Kool J, Slagboom J. Acetylcholine-Binding Protein Affinity Profiling of Neurotoxins in Snake Venoms with Parallel Toxin Identification. Int J Mol Sci 2023; 24:16769. [PMID: 38069093 PMCID: PMC10706727 DOI: 10.3390/ijms242316769] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Snakebite is considered a concerning issue and a neglected tropical disease. Three-finger toxins (3FTxs) in snake venoms primarily cause neurotoxic effects since they have high affinity for nicotinic acetylcholine receptors (nAChRs). Their small molecular size makes 3FTxs weakly immunogenic and therefore not appropriately targeted by current antivenoms. This study aims at presenting and applying an analytical method for investigating the therapeutic potential of the acetylcholine-binding protein (AChBP), an efficient nAChR mimic that can capture 3FTxs, for alternative treatment of elapid snakebites. In this analytical methodology, snake venom toxins were separated and characterised using high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS) and high-throughput venomics. By subsequent nanofractionation analytics, binding profiling of toxins to the AChBP was achieved with a post-column plate reader-based fluorescence-enhancement ligand displacement bioassay. The integrated method was established and applied to profiling venoms of six elapid snakes (Naja mossambica, Ophiophagus hannah, Dendroaspis polylepis, Naja kaouthia, Naja haje and Bungarus multicinctus). The methodology demonstrated that the AChBP is able to effectively bind long-chain 3FTxs with relatively high affinity, but has low or no binding affinity towards short-chain 3FTxs, and as such provides an efficient analytical platform to investigate binding affinity of 3FTxs to the AChBP and mutants thereof and to rapidly identify bound toxins.
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Affiliation(s)
- Giulia Palermo
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands; (G.P.); (W.M.S.); (L.L.A.)
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Wietse M. Schouten
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands; (G.P.); (W.M.S.); (L.L.A.)
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Luis Lago Alonso
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands; (G.P.); (W.M.S.); (L.L.A.)
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Chris Ulens
- Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium;
| | - Jeroen Kool
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands; (G.P.); (W.M.S.); (L.L.A.)
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Julien Slagboom
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands; (G.P.); (W.M.S.); (L.L.A.)
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
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3
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Otvos RA, Still KBM, Somsen GW, Smit AB, Kool J. Drug Discovery on Natural Products: From Ion Channels to nAChRs, from Nature to Libraries, from Analytics to Assays. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2019; 24:362-385. [PMID: 30682257 PMCID: PMC6484542 DOI: 10.1177/2472555218822098] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/16/2018] [Accepted: 12/07/2018] [Indexed: 12/21/2022]
Abstract
Natural extracts are complex mixtures that may be rich in useful bioactive compounds and therefore are attractive sources for new leads in drug discovery. This review describes drug discovery from natural products and in explaining this process puts the focus on ion-channel drug discovery. In particular, the identification of bioactives from natural products targeting nicotinic acetylcholine receptors (nAChRs) and serotonin type 3 receptors (5-HT3Rs) is discussed. The review is divided into three parts: "Targets," "Sources," and "Approaches." The "Targets" part will discuss the importance of ion-channel drug targets in general, and the α7-nAChR and 5-HT3Rs in particular. The "Sources" part will discuss the relevance for drug discovery of finding bioactive compounds from various natural sources such as venoms and plant extracts. The "Approaches" part will give an overview of classical and new analytical approaches that are used for the identification of new bioactive compounds with the focus on targeting ion channels. In addition, a selected overview is given of traditional venom-based drug discovery approaches and of diverse hyphenated analytical systems used for screening complex bioactive mixtures including venoms.
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Affiliation(s)
- Reka A. Otvos
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kristina B. M. Still
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Govert W. Somsen
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jeroen Kool
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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4
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Xiao H, Brinkmann M, Thalmann B, Schiwy A, Große Brinkhaus S, Achten C, Eichbaum K, Gembé C, Seiler TB, Hollert H. Toward Streamlined Identification of Dioxin-like Compounds in Environmental Samples through Integration of Suspension Bioassay. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:3382-3390. [PMID: 28190338 DOI: 10.1021/acs.est.6b06003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Effect-directed analysis (EDA) is a powerful strategy to identify biologically active compounds in environmental samples. However, in current EDA studies, fractionation and handling procedures are laborious, consist of multiple evaporation steps, and thus bear the risk of contamination and decreased recoveries of the target compounds. The low resulting throughput has been one of the major bottlenecks of EDA. Here, we propose a high-throughput EDA (HT-EDA) work-flow combining reversed phase high-performance liquid chromatography fractionation of samples into 96-well microplates, followed by toxicity assessment in the micro-EROD bioassay with the wild-type rat hepatoma H4IIE cells, and chemical analysis of bioactive fractions. The approach was evaluated using single substances, binary mixtures, and extracts of sediment samples collected at the Three Gorges Reservoir, Yangtze River, China, as well as the rivers Rhine and Elbe, Germany. Selected bioactive fractions were analyzed by highly sensitive gas chromatography-atmospheric pressure laser ionization-time-of-flight-mass spectrometry. In addition, we optimized the work-flow by seeding previously adapted suspension-cultured H4IIE cells directly into the microplate used for fractionation, which makes any transfers of fractionated samples unnecessary. The proposed HT-EDA work-flow simplifies the procedure for wider application in ecotoxicology and environmental routine programs.
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Affiliation(s)
| | - Markus Brinkmann
- Toxicology Centre and School of Environment and Sustainability, University of Saskatchewan , Saskatoon, Saskatchewan S7N 5B3, Canada
| | | | | | - Sigrid Große Brinkhaus
- Institute of Geology and Palaeontology-Applied Geology, University of Münster , 48149 Münster, Germany
| | - Christine Achten
- Institute of Geology and Palaeontology-Applied Geology, University of Münster , 48149 Münster, Germany
| | | | | | | | - Henner Hollert
- College of Resources and Environmental Science, Chongqing University , 400030 Chongqing, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , 210023 Nanjing, China
- College of Environmental Science and Engineering and State Key Laboratory of Pollution Control and Resource Reuse, Tongji University , 200092 Shanghai, China
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5
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Brack W, Dulio V, Ågerstrand M, Allan I, Altenburger R, Brinkmann M, Bunke D, Burgess RM, Cousins I, Escher BI, Hernández FJ, Hewitt LM, Hilscherová K, Hollender J, Hollert H, Kase R, Klauer B, Lindim C, Herráez DL, Miège C, Munthe J, O'Toole S, Posthuma L, Rüdel H, Schäfer RB, Sengl M, Smedes F, van de Meent D, van den Brink PJ, van Gils J, van Wezel AP, Vethaak AD, Vermeirssen E, von der Ohe PC, Vrana B. Towards the review of the European Union Water Framework Directive: Recommendations for more efficient assessment and management of chemical contamination in European surface water resources. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 576:720-737. [PMID: 27810758 PMCID: PMC8281610 DOI: 10.1016/j.scitotenv.2016.10.104] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/14/2016] [Accepted: 10/15/2016] [Indexed: 05/21/2023]
Abstract
Water is a vital resource for natural ecosystems and human life, and assuring a high quality of water and protecting it from chemical contamination is a major societal goal in the European Union. The Water Framework Directive (WFD) and its daughter directives are the major body of legislation for the protection and sustainable use of European freshwater resources. The practical implementation of the WFD with regard to chemical pollution has faced some challenges. In support of the upcoming WFD review in 2019 the research project SOLUTIONS and the European monitoring network NORMAN has analyzed these challenges, evaluated the state-of-the-art of the science and suggested possible solutions. We give 10 recommendations to improve monitoring and to strengthen comprehensive prioritization, to foster consistent assessment and to support solution-oriented management of surface waters. The integration of effect-based tools, the application of passive sampling for bioaccumulative chemicals and an integrated strategy for prioritization of contaminants, accounting for knowledge gaps, are seen as important approaches to advance monitoring. Including all relevant chemical contaminants in more holistic "chemical status" assessment, using effect-based trigger values to address priority mixtures of chemicals, to better consider historical burdens accumulated in sediments and to use models to fill data gaps are recommended for a consistent assessment of contamination. Solution-oriented management should apply a tiered approach in investigative monitoring to identify toxicity drivers, strengthen consistent legislative frameworks and apply solutions-oriented approaches that explore risk reduction scenarios before and along with risk assessment.
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Affiliation(s)
- Werner Brack
- Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany; RWTH Aachen University, Aachen, Germany.
| | - Valeria Dulio
- Institut National de l'Environnement Industriel et des Risques INERIS, Verneuil-en-Halatte, France
| | - Marlene Ågerstrand
- ACES - Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
| | - Ian Allan
- Norwegian Institute for Water Research (NIVA), Oslo, Norway
| | - Rolf Altenburger
- Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany; RWTH Aachen University, Aachen, Germany
| | | | - Dirk Bunke
- Oeko-Institut e.V. - Institute for Applied Ecology, Freiburg, Germany
| | - Robert M Burgess
- U.S. Environmental Protection Agency, ORD, NHEERL, Atlantic Ecology Division, Narrangansett, RI, USA
| | - Ian Cousins
- ACES - Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
| | - Beate I Escher
- Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany; Eberhard Karls University of Tübingen, Tübingen, Germany
| | | | - L Mark Hewitt
- Aquatic Ecosystem Protection Research Division, Environment Canada, Burlington, Ontario, Canada
| | - Klára Hilscherová
- Masaryk University, Research Centre for Toxic Compounds in the Environment (RECETOX), Brno, Czech Republic
| | - Juliane Hollender
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | | | - Robert Kase
- Swiss Centre for Applied Ecotoxicology, Eawag-EPFL, Dübendorf, Switzerland
| | - Bernd Klauer
- Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany
| | - Claudia Lindim
- ACES - Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
| | | | - Cécil Miège
- IRSTEA - UR MALY, Villeurbanne Cedex, France
| | - John Munthe
- IVL Swedish Environmental Research Institute, Gothenburg, Sweden
| | | | - Leo Posthuma
- National Institute for Public Health and the Environment RIVM, Bilthoven, The Netherlands; Department of Environmental Science, Institute for Water and Wetland Research, Radboud University Nijmegen, The Netherlands
| | - Heinz Rüdel
- Fraunhofer Inst Mol Biol & Appl Ecol IME, Aberg 1, D-57392 Schmallenberg, Germany
| | | | - Manfred Sengl
- Bavarian Environmental Agency, D-86179 Augsburg, Germany
| | - Foppe Smedes
- Masaryk University, Research Centre for Toxic Compounds in the Environment (RECETOX), Brno, Czech Republic
| | | | - Paul J van den Brink
- Alterra, Wageningen University and Research Centre, P.O. Box 47, 6700 AA Wageningen, The Netherlands; Department of Aquatic Ecology and Water Quality Management, Wageningen University and Research Centre, P.O. Box 47, 6700 AA Wageningen, The Netherlands
| | | | - Annemarie P van Wezel
- KWR Watercycle Research Institute, Nieuwegein, The Netherlands; Copernicus Institute, Utrecht University, Utrecht, The Netherlands
| | - A Dick Vethaak
- Deltares, Delft, The Netherlands; VU University Amsterdam, Institute for Environmental Studies, Amsterdam, The Netherlands
| | - Etienne Vermeirssen
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | | | - Branislav Vrana
- Masaryk University, Research Centre for Toxic Compounds in the Environment (RECETOX), Brno, Czech Republic
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6
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Otvos RA, van Nierop P, Niessen WMA, Kini RM, Somsen GW, Smit AB, Kool J. Development of an Online Cell-Based Bioactivity Screening Method by Coupling Liquid Chromatography to Flow Cytometry with Parallel Mass Spectrometry. Anal Chem 2016; 88:4825-32. [DOI: 10.1021/acs.analchem.6b00455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Reka A. Otvos
- Division
of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
- Department
of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Pim van Nierop
- Department
of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Wilfried M. A. Niessen
- Division
of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
- hyphen MassSpec, Herenweg 95, 2361
EK Warmond, The Netherlands
| | - R. Manjunatha Kini
- Department
of Biological Sciences, National University of Singapore, 14 Science
Drive 4, 117543, Singapore
| | - Govert W. Somsen
- Division
of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
| | - August B. Smit
- Department
of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Jeroen Kool
- Division
of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
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7
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Brack W, Ait-Aissa S, Burgess RM, Busch W, Creusot N, Di Paolo C, Escher BI, Mark Hewitt L, Hilscherova K, Hollender J, Hollert H, Jonker W, Kool J, Lamoree M, Muschket M, Neumann S, Rostkowski P, Ruttkies C, Schollee J, Schymanski EL, Schulze T, Seiler TB, Tindall AJ, De Aragão Umbuzeiro G, Vrana B, Krauss M. Effect-directed analysis supporting monitoring of aquatic environments--An in-depth overview. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 544:1073-118. [PMID: 26779957 DOI: 10.1016/j.scitotenv.2015.11.102] [Citation(s) in RCA: 250] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/20/2015] [Accepted: 11/20/2015] [Indexed: 05/18/2023]
Abstract
Aquatic environments are often contaminated with complex mixtures of chemicals that may pose a risk to ecosystems and human health. This contamination cannot be addressed with target analysis alone but tools are required to reduce this complexity and identify those chemicals that might cause adverse effects. Effect-directed analysis (EDA) is designed to meet this challenge and faces increasing interest in water and sediment quality monitoring. Thus, the present paper summarizes current experience with the EDA approach and the tools required, and provides practical advice on their application. The paper highlights the need for proper problem formulation and gives general advice for study design. As the EDA approach is directed by toxicity, basic principles for the selection of bioassays are given as well as a comprehensive compilation of appropriate assays, including their strengths and weaknesses. A specific focus is given to strategies for sampling, extraction and bioassay dosing since they strongly impact prioritization of toxicants in EDA. Reduction of sample complexity mainly relies on fractionation procedures, which are discussed in this paper, including quality assurance and quality control. Automated combinations of fractionation, biotesting and chemical analysis using so-called hyphenated tools can enhance the throughput and might reduce the risk of artifacts in laboratory work. The key to determining the chemical structures causing effects is analytical toxicant identification. The latest approaches, tools, software and databases for target-, suspect and non-target screening as well as unknown identification are discussed together with analytical and toxicological confirmation approaches. A better understanding of optimal use and combination of EDA tools will help to design efficient and successful toxicant identification studies in the context of quality monitoring in multiply stressed environments.
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Affiliation(s)
- Werner Brack
- UFZ Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany; RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Selim Ait-Aissa
- Institut National de l'Environnement Industriel et des Risques INERIS, BP2, 60550 Verneuil-en-Halatte, France
| | - Robert M Burgess
- US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Narragansett, RI, USA
| | - Wibke Busch
- UFZ Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Nicolas Creusot
- Institut National de l'Environnement Industriel et des Risques INERIS, BP2, 60550 Verneuil-en-Halatte, France
| | | | - Beate I Escher
- UFZ Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany; Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - L Mark Hewitt
- Water Science and Technology Directorate, Environment Canada, 867 Lakeshore Road, Burlington, Ontario L7S 1A1, Canada
| | - Klara Hilscherova
- Masaryk University, Research Centre for Toxic Compounds in the Environment (RECETOX), Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Juliane Hollender
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Henner Hollert
- RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Willem Jonker
- VU University, BioMolecular Analysis Group, Amsterdam, The Netherlands
| | - Jeroen Kool
- VU University, BioMolecular Analysis Group, Amsterdam, The Netherlands
| | - Marja Lamoree
- VU Amsterdam, Institute for Environmental Studies, Amsterdam, The Netherlands
| | - Matthias Muschket
- UFZ Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Pawel Rostkowski
- NILU - Norwegian Institute for Air Research, Instituttveien 18, 2007 Kjeller, Norway
| | | | - Jennifer Schollee
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Emma L Schymanski
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Tobias Schulze
- UFZ Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | | | - Andrew J Tindall
- WatchFrag, Bâtiment Genavenir 3, 1 Rue Pierre Fontaine, 91000 Evry, France
| | | | - Branislav Vrana
- Masaryk University, Research Centre for Toxic Compounds in the Environment (RECETOX), Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Martin Krauss
- UFZ Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
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8
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Rapid activity-directed screening of estrogens by parallel coupling of liquid chromatography with a functional gene reporter assay and mass spectrometry. J Chromatogr A 2015; 1406:165-74. [DOI: 10.1016/j.chroma.2015.06.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/04/2015] [Accepted: 06/07/2015] [Indexed: 02/02/2023]
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9
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Stornaiuolo M, De Kloe GE, Rucktooa P, Fish A, van Elk R, Edink ES, Bertrand D, Smit AB, de Esch IJP, Sixma TK. Assembly of a π-π stack of ligands in the binding site of an acetylcholine-binding protein. Nat Commun 2013; 4:1875. [PMID: 23695669 PMCID: PMC3674282 DOI: 10.1038/ncomms2900] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 04/17/2013] [Indexed: 12/11/2022] Open
Abstract
Acetylcholine-binding protein is a water-soluble homologue of the extracellular ligand-binding domain of cys-loop receptors. It is used as a structurally accessible prototype for studying ligand binding to these pharmaceutically important pentameric ion channels, in particular to nicotinic acetylcholine receptors, due to conserved binding site residues present at the interface between two subunits. Here we report that an aromatic conjugated small molecule binds acetylcholine-binding protein in an ordered π-π stack of three identical molecules per binding site, two parallel and one antiparallel. Acetylcholine-binding protein stabilizes the assembly of the stack by aromatic contacts. Thanks to the plasticity of its ligand-binding site, acetylcholine-binding protein can accommodate the formation of aromatic stacks of different size by simple loop repositioning and minimal adjustment of the interactions. This type of supramolecular binding provides a novel paradigm in drug design.
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Affiliation(s)
- Mariano Stornaiuolo
- Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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10
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Potterat O, Hamburger M. Concepts and technologies for tracking bioactive compounds in natural product extracts: generation of libraries, and hyphenation of analytical processes with bioassays. Nat Prod Rep 2013; 30:546-64. [DOI: 10.1039/c3np20094a] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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11
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Kool J, Rudebeck A, Fleurbaaij F, Nijmeijer S, Falck D, Smits R, Vischer H, Leurs R, Niessen W. High-resolution metabolic profiling towards G protein-coupled receptors: Rapid and comprehensive screening of histamine H4 receptor ligands. J Chromatogr A 2012; 1259:213-20. [DOI: 10.1016/j.chroma.2012.03.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 03/12/2012] [Accepted: 03/13/2012] [Indexed: 10/28/2022]
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12
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Weller MG. A unifying review of bioassay-guided fractionation, effect-directed analysis and related techniques. SENSORS 2012; 12:9181-209. [PMID: 23012539 PMCID: PMC3444097 DOI: 10.3390/s120709181] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/26/2012] [Accepted: 07/02/2012] [Indexed: 12/24/2022]
Abstract
The success of modern methods in analytical chemistry sometimes obscures the problem that the ever increasing amount of analytical data does not necessarily give more insight of practical relevance. As alternative approaches, toxicity- and bioactivity-based assays can deliver valuable information about biological effects of complex materials in humans, other species or even ecosystems. However, the observed effects often cannot be clearly assigned to specific chemical compounds. In these cases, the establishment of an unambiguous cause-effect relationship is not possible. Effect-directed analysis tries to interconnect instrumental analytical techniques with a biological/biochemical entity, which identifies or isolates substances of biological relevance. Successful application has been demonstrated in many fields, either as proof-of-principle studies or even for complex samples. This review discusses the different approaches, advantages and limitations and finally shows some practical examples. The broad emergence of effect-directed analytical concepts might lead to a true paradigm shift in analytical chemistry, away from ever growing lists of chemical compounds. The connection of biological effects with the identification and quantification of molecular entities leads to relevant answers to many real life questions.
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Affiliation(s)
- Michael G Weller
- Division 1.5 Protein Analysis, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Strasse 11, 12489 Berlin, Germany.
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Nijmeijer S, Vischer HF, Rudebeck AF, Fleurbaaij F, Falck D, Leurs R, Niessen WMA, Kool J. Development of a profiling strategy for metabolic mixtures by combining chromatography and mass spectrometry with cell-based GPCR signaling. ACTA ACUST UNITED AC 2012; 17:1329-38. [PMID: 22740245 DOI: 10.1177/1087057112451922] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this study, we developed an in-line methodology that combines analytical with pharmacological techniques to characterize metabolites of human histamine H(4) receptor (hH(4)R) ligands. Liquid chromatographic separation of metabolic mixtures is coupled to high-resolution fractionation into 96- or 384-well plates and directly followed by a cell-based reporter gene assay to measure receptor signaling. The complete methodology was designed, optimized, validated, and ultimately miniaturized into a high-density well plate format. Finally, the methodology was demonstrated in a metabolic profiling setting for three hH(4)R lead compounds and the drug clozapine. This new methodology comprises integrated analytical separations, mass spectrometry, and a cell-based signal transduction-driven reporter gene assay that enables the implementation of comprehensive metabolic profiling earlier in the drug discovery process.
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Affiliation(s)
- Saskia Nijmeijer
- Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University, Amsterdam, The Netherlands
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Development of on-line high performance liquid chromatography (HPLC)-biochemical detection methods as tools in the identification of bioactives. Int J Mol Sci 2012; 13:3101-3133. [PMID: 22489144 PMCID: PMC3317705 DOI: 10.3390/ijms13033101] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 02/08/2012] [Accepted: 03/01/2012] [Indexed: 11/23/2022] Open
Abstract
Biochemical detection (BCD) methods are commonly used to screen plant extracts for specific biological activities in batch assays. Traditionally, bioactives in the most active extracts were identified through time-consuming bio-assay guided fractionation until single active compounds could be isolated. Not only are isolation procedures often tedious, but they could also lead to artifact formation. On-line coupling of BCD assays to high performance liquid chromatography (HPLC) is gaining ground as a high resolution screening technique to overcome problems associated with pre-isolation by measuring the effects of compounds post-column directly after separation. To date, several on-line HPLC-BCD assays, applied to whole plant extracts and mixtures, have been published. In this review the focus will fall on enzyme-based, receptor-based and antioxidant assays.
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Utsintong M, Rojsanga P, Ho KY, Talley TT, Olson AJ, Matsumoto K, Vajragupta O. Virtual screening against acetylcholine binding protein. ACTA ACUST UNITED AC 2011; 17:204-15. [PMID: 21956172 DOI: 10.1177/1087057111421667] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The nicotinic acetylcholine receptors (nAChRs) are a member of the ligand-gated ion channel family and play a key role in the transfer of information across neurological networks. The X-ray crystal structure of agonist-bound α(7) acetylcholine binding protein (AChBP) has been recognized as the most appropriate template to model the ligand-binding domain of nAChR for studying the molecular mechanism of the receptor-ligand interactions. Virtual screening of the National Cancer Institute diversity set, a library of 1990 compounds with nonredundant pharmacophore profiles, using AutoDock against AChBPs revealed 51 potential candidates. In vitro radioligand competition assays using [(3)H] epibatidine against the AChBPs from the freshwater snails, Lymnaea stagnalis, and from the marine species, Aplysia californica and the mutant (AcY55W), revealed seven compounds from the list of candidates that had micromolar to nanomolar affinities for the AChBPs. Further investigation on α(7)nAChR expressing in Xenopus oocytes and on the recombinant receptors with fluorescence resonance energy transfer (FRET)-based calcium sensor expressing in HEK cells showed that seven compounds were antagonists of α(7)nAChR, only one compound (NSC34352) demonstrated partial agonistic effect at low dose (10 µM), and two compounds (NSC36369 and NSC34352) were selective antagonists on α(7)nAchR with moderate potency. These hits serve as novel templates/scaffolds for development of more potent and specific in the AChR systems.
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Affiliation(s)
- Maleeruk Utsintong
- School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand
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